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Next-generation sequencing

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https://www.readbyqxmd.com/read/28549094/a-novel-dominant-mutation-in-sag-the-arrestin-1-gene-is-a-common-cause-of-retinitis-pigmentosa-in-hispanic-families-in-the-southwestern-united-states
#1
Lori S Sullivan, Sara J Bowne, Daniel C Koboldt, Elizabeth L Cadena, John R Heckenlively, Kari E Branham, Dianna H Wheaton, Kaylie D Jones, Richard S Ruiz, Mark E Pennesi, Paul Yang, David Davis-Boozer, Hope Northrup, Vsevold V Gurevich, Rui Chen, Mingchu Xu, Yumei Li, David G Birch, Stephen P Daiger
Purpose: To identify the causes of autosomal dominant retinitis pigmentosa (adRP) in a cohort of families without mutations in known adRP genes and consequently to characterize a novel dominant-acting missense mutation in SAG. Methods: Patients underwent ophthalmologic testing and were screened for mutations using targeted-capture and whole-exome next-generation sequencing. Confirmation and additional screening were done by Sanger sequencing. Haplotypes segregating with the mutation were determined using short tandem repeat and single nucleotide variant polymorphisms...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28548292/hypertriglyceridemic-acute-pancreatitis-in-an-emergency-department-the-typical-clinical-features-and-genetic-variants
#2
Wan Jun Chen, Xiao Fan Sun, Rui Xue Zhang, Min Jie Xu, Tong Hai Dou, Xiao Bin Zhang, Min Zhong, Wei Qiang Yang, Li Liu, Xiao Ye Lu, Chang Qing Zhu
OBJECTIVE: To investigate the clinical characteristics of hypertriglyceridemic acute pancreatitis (HTGAP), and the molecular foundation contributing to the hypertriglyceridemia in this group of patients. METHODS: Clinical data from 329 patients with AP were collected and analyzed. All the patients were divided into 1) HTGAP group (n = 40), with fasting serum triglyceride ≥ 500 mg/dL; and 2) NHTGAP group (n = 289). Next, the targeted next-generation sequencing was applied in 11 HTGAP patients to detect the genetic mutation associated with hypertriglyceridemia that included apolipoprotein A-5 (APOA5), apolipoprotein C-3 (APOC3), apolipoprotein E (APOE), BLK proto-oncogene, lipoprotein lipase (LPL), apolipoprotein C-2 (APOC2), glycosylphosphatidylinositol anchored high density lipoprotein binding protein-1(GPIHBP1), and lipase maturation factor-1(LMF1)...
May 26, 2017: Journal of Digestive Diseases
https://www.readbyqxmd.com/read/28548125/next-generation-sequencing-based-molecular-characterization-of-primary-urinary-bladder-adenocarcinoma
#3
Somak Roy, Dinesh Pradhan, Wayne L Ernst, Stephanie Mercurio, Yana Najjar, Rahul Parikh, Anil V Parwani, Reetesh K Pai, Rajiv Dhir, Marina N Nikiforova
Primary bladder adenocarcinoma is a rare and aggressive tumor with poor clinical outcomes and no standard of care therapy. Molecular biology of this tumor is unknown due to the lack of comprehensive molecular profiling studies. The study aimed to identify genomic alterations of clinical and therapeutic significance using next-generation sequencing and compare genomic profile of primary bladder adenocarcinoma with that of high-grade urothelial carcinoma and colorectal adenocarcinoma. A cohort of 15 well-characterized primary bladder adenocarcinoma was subjected to targeted next-generation sequencing for the identification of mutations and copy-number changes in 51 cancer-related genes...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28548121/ebv-negative-aggressive-nk-cell-leukemia-lymphoma-a-clinical-and-pathological-study-from-a-single-institution
#4
Juehua Gao, Amir Behdad, Peng Ji, Kristy L Wolniak, Olga Frankfurt, Yi-Hua Chen
Aggressive natural killer (NK)-cell leukemia/lymphoma is a systemic NK-cell neoplasm that preferentially affects Asians with a fulminant clinical course and is almost always associated with Epstein-Barr virus (EBV). The data on EBV-negative aggressive NK-cell leukemia/lymphoma are limited. Here we report a series of three patients (two Caucasians, one African-American) with EBV-negative aggressive NK-cell leukemia/lymphoma from a single institution, including a case diagnosed on post-mortem examination. Similar to EBV-positive aggressive NK-cell leukemia/lymphoma, our patients presented with constitutional symptoms and hepatosplenomegaly, and followed a highly aggressive clinical course...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28548082/whole-genome-sequencing-and-imputation-in-isolated-populations-identify-genetic-associations-with-medically-relevant-complex-traits
#5
Lorraine Southam, Arthur Gilly, Dániel Süveges, Aliki-Eleni Farmaki, Jeremy Schwartzentruber, Ioanna Tachmazidou, Angela Matchan, Nigel W Rayner, Emmanouil Tsafantakis, Maria Karaleftheri, Yali Xue, George Dedoussis, Eleftheria Zeggini
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#6
V Albrecht, C Zweiniger, V Surendranath, K Lang, G Schöfl, A Dahl, S Winkler, V Lange, I Böhme, A H Schmidt
The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences...
May 25, 2017: HLA
https://www.readbyqxmd.com/read/28547571/clinical-presentations-and-molecular-studies-of-invasive-renal-epithelioid-angiomyolipoma
#7
Cheng-Keng Chuang, Hsin Chia Angela Lin, Han-Yu Tasi, Kun-Han Lee, Yuting Kao, Fukai Leo Chuang, Ying-Hsu Chang, Po-Hung Lin, Chung-Yi Liu, See-Tong Pang
PURPOSE: Epithelioid angiomyolipoma (EAML) is a rare variant of renal angiomyolipoma with malignant potential, and the cytogenetic and clinical behavior of EAML remains a challenging issue. METHODS: We retrospectively analyze the clinical courses of five EAML, the use of everolimus on metastatic EAML, and next-generation sequencing (NGS) and polymerase chain reaction (PCR) studies to investigate the gene mutation of TSC and the impact of PI3K/Akt/mTOR signaling pathway in metastatic EAML...
May 25, 2017: International Urology and Nephrology
https://www.readbyqxmd.com/read/28547568/biofertilizers-and-sustainable-agriculture-exploring-arbuscular-mycorrhizal-fungi
#8
REVIEW
Nicholas O Igiehon, Olubukola O Babalola
Worldwide agricultural food production has to double in 2050 so as to feed the global increasing population while reducing dependency on conventional chemical fertilizers plus pesticides. To accomplish this objective, there is the need to explore the several mutualistic interactions between plant roots and rhizosphere microbiome. Biofertilization is the process of boosting the abundance of microorganisms such as arbuscular mycorrhizal fungi (AMF) in the natural plant rhizosphere which depicts a beneficial alternative to chemical fertilization practices...
May 25, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28547382/comparative-analysis-of-cherry-virus-a-genome-sequences-assembled-from-deep-sequencing-data
#9
Prasad Kesanakurti, Mark Belton, Hanaa Saeed, Heidi Rast, Ian Boyes, Michael Rott
Cherry virus A (CVA) is a ubiquitous graft-transmissible virus that mainly infects Prunus spp. Next-generation sequencing was applied to 39 tree fruit specimens infected with CVA, and 75 full and 16 partial-length CVA genome sequences were assembled. Phylogenetic analysis of these and 11 previously sequenced CVA genomes resulted in six major clusters with no observable relationship between the host and the assembled genome sequences. Recombination analysis detected four recombinants. Consistent single-nucleotide polymorphism (SNP) patterns were observed between the 75 full-length genomes and their sequence clouds, which supports a quasispecies model for CVA evolution...
May 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28546993/nationwide-genetic-analysis-for-molecularly-unresolved-cystic-fibrosis-patients-in-a-multiethnic-society-implications-for-preconception-carrier-screening
#10
Doron M Behar, Ori Inbar, Michal Shteinberg, Michal Gur, Huda Mussaffi, David Shoseyov, Moshe Ashkenazi, Soliman Alkrinawi, Concetta Bormans, Fahed Hakim, Meir Mei-Zahav, Malena Cohen-Cymberknoh, Adi Dagan, Dario Prais, Ifat Sarouk, Patrick Stafler, Bat El Bar Aluma, Gidon Akler, Elie Picard, Micha Aviram, Ori Efrati, Galit Livnat, Joseph Rivlin, Lea Bentur, Hannah Blau, Eitan Kerem, Amihood Singer
BACKGROUND: Preconception carrier screening for cystic fibrosis (CF) is usually performed using ethnically targeted panels of selected mutations. This has been recently challenged by the use of expanded, ethnically indifferent, pan-population panels. Israel is characterized by genetically heterogeneous populations carrying a wide range of CFTR mutations. To assess the potential of expanding the current Israeli preconception screening program, we sought the subset of molecularly unresolved CF patients listed in the Israeli CF data registry comprising ~650 patients...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546554/high-throughput-resistance-profiling-of-plasmodium-falciparum-infections-based-on-custom-dual-indexing-and-illumina-next-generation-sequencing-technology
#11
Sidsel Nag, Marlene D Dalgaard, Poul-Erik Kofoed, Johan Ursing, Marina Crespo, Lee O'Brien Andersen, Frank Møller Aarestrup, Ole Lund, Michael Alifrangis
Genetic polymorphisms in P. falciparum can be used to indicate the parasite's susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin...
May 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28546553/symbiont-community-stability-through-severe-coral-bleaching-in-a-thermally-extreme-lagoon
#12
E G Smith, G O Vaughan, R N Ketchum, D McParland, J A Burt
Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals' responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C, Min = 16...
May 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28546527/effect-of-necrosis-on-the-mirna-mrna-regulatory-network-in-crt-mg-human-astroglioma-cells
#13
So-Hee Ahn, Jung-Hyuck Ahn, Dong-Ryeol Ryu, Jisoo Lee, Min-Sun Cho, Youn-Hee Choi
Purpose: Glioblastoma multiforme (GBM) is the most common adult primary intracranial tumor. The remarkable features of GBM include central necrosis. MicroRNAs (miRNAs) have been considered as diagnostic/prognostic biomarkers for many cancers, including glioblastoma. However, the effect of necrosis on the miRNA expression profile and predicted miRNA-mRNA regulatory information remain unclear. The purpose of this study is to examine the effect of necrotic cells on the modulation of miRNA and mRNA expression profiles and miRNA-mRNA network in CRT-MG cells...
May 22, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28546435/a-simple-pipeline-for-mapping-point-mutations
#14
Guy Wachsman, Jennifer L Modliszewski, Manuel Valdes, Philip N Benfey
A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost-efficiency and ease of data production afforded by next-generation sequencing has created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user-friendly, complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes...
May 25, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28545961/pecc-correcting-contigs-based-on-paired-end-read-distribution
#15
Min Li, Binbin Wu, Xiaodong Yan, Junwei Luo, Yi Pan, Fang-Xiang Wu, Jianxin Wang
MOTIVATION: Cheap and fast next generation sequencing (NGS) technologies facilitate research of de novo assembly greatly. The reliability of contigs is critical to construct reliable scaffolding. However, contigs generated from most assemblers contain errors because of the limitation of assembly strategy and computation complexity. Among all these errors, the misassembly error is one of the most harmful types. RESULTS: In this paper, we propose a new method named "PECC" to identify and correct misassembly errors in contigs based on the paired-end read distribution...
May 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28545654/genetic-approach-to-ambiguous-genitalia-and-disorders-of-sex-development-what-clinicians-need-to-know
#16
Svetlana A Yatsenko, Selma Feldman Witchel
Genetic tools such as microarray and next-generation sequencing have initiated a new era for the diagnosis and management of patients with disorders of sex development (DSDs). These tools supplement the traditional approach to the evaluation and care of infants, children, and adolescents with DSDs. These tests can detect genetic variations known to be associated with DSDs, discover novel genetic variants, and elucidate novel mechanisms of gene regulation. Herein, we discuss these tests and their role in the management of patients with DSDs...
May 22, 2017: Seminars in Perinatology
https://www.readbyqxmd.com/read/28545403/long-lasting-effect-of-obesity-on-skeletal-muscle-transcriptome
#17
Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S Park, Suzanne S Fei, Hollis Wright, Ashley E White, Ruhee Jain, Judy L Cameron, Kerri M Winters-Stone, Oleg Varlamov
BACKGROUND: Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene expression, contributing to long-term obesity complications. While caloric restriction can reduce obesity and glucose intolerance, it is currently unknown whether it can effectively reprogram transcriptome to a pre-obesity level. The present study addressed this question by the preliminary examination of the transcriptional dynamics in skeletal muscle after exposure to overnutrition and following caloric restriction...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#18
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545106/serum-microrna-signatures-as-liquid-biopsies-for-interrogating-hepatotoxic-mechanisms-and-liver-pathogenesis-in-human
#19
Julian Krauskopf, Theo M de Kok, Shelli J Schomaker, Mark Gosink, Deborah A Burt, Patricia Chandler, Roscoe L Warner, Kent J Johnson, Florian Caiment, Jos C Kleinjans, Jiri Aubrecht
MicroRNAs (miRNAs) released into the peripheral circulation upon cellular injury have shown a promise as a new class of tissue-specific biomarkers. We were first to demonstrate that next-generation sequencing analysis of serum from human subjects with acetaminophen-induced liver injury revealed a specific signature of circulating miRNAs. We consequently hypothesized that different types of hepatic liver impairments might feature distinct signatures of circulating miRNAs and that this approach might be useful as minimally invasive diagnostic "liquid biopsies" enabling the interrogation of underlying molecular mechanisms of injury in distant tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28545050/prevalence-and-extent-of-heteroresistance-by-next-generation-sequencing-of-multidrug-resistant-tuberculosis
#20
Darwin J Operario, Alexander F Koeppel, Stephen D Turner, Yongde Bao, Suporn Pholwat, Sayera Banu, Suporn Foongladda, Stellah Mpagama, Jean Gratz, Oleg Ogarkov, Svetlana Zhadova, Scott K Heysell, Eric R Houpt
Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides. Across these gene regions, complete resistance or heteroresistance (defined as 1%-99% mutation) was present in at least one isolate in 6.3% of loci. The number of isolates with heteroresistance was highest for gyrA codon 94, rpoB codons 526 and 531, and embB codons 306, 372 and 406 (range 11-26% of isolates exhibited heteroresistance)...
2017: PloS One
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